León-Castillo et al. 2020 custom POLE framework · vleon-castillo-2020-custom-framework-v1
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POLE encodes the catalytic subunit of DNA polymerase epsilon, the enzyme that replicates the leading strand of DNA during cell division and participates in DNA repair. It contains a proofreading domain that corrects replication errors, keeping the accumulation of mutations in check. Germline mutations in POLE cause polyposis and predispose to colorectal cancer, and are also linked to a rare syndrome of facial dysmorphism, immunodeficiency, livedo, and short stature. Somatic mutations, particularly in the proofreading domain, occur in colorectal and endometrial cancers, where they drive an ultra-mutated tumor phenotype and are associated with better responses to immune checkpoint inhibitors.
This variant
POLE germline variants predispose to polyposis and colorectal cancer, mostly through missense changes in the proofreading (exonuclease) domain. This variant is a synonymous change (p.Ser988=) in exon 25, outside that domain, with no predicted splice impact. Its VUS classification reflects that it does not match the gene's established disease mechanism, while population-frequency and functional evidence needed for a benign call are lacking.
Transcript
NM_006231.4
HGVS · transcript:coding
NM_006231.4:c.2964G>T
GRCh38
chr12:132661065 C>A
GRCh37
chr12:133237651 C>A
VUS: only two supporting criteria are met — PM2 (absent from all population databases) and BP7 (synonymous, no splice impact) — which conflict and satisfy no enumerated combination.
Classification rationale
PM2BP7VUS
POLE c.2964G>Tmissense
PM2 (Supporting): absent from gnomAD v2.1, v4.1, and gnomAD-Canada — no carriers in large control populations. BP7 (Supporting): synonymous p.Ser988= with SpliceAI max delta 0.01, predicting no splice impact. Overall: VUS — the conflicting PM2 and BP7 supporting evidence satisfies no enumerated Pathogenic, Likely Pathogenic, Benign, or Likely Benign combination.
PM2 + BP7→VUS
LYFE Sciences is an AI system, and it can make mistakes. Criteria
may be applied incorrectly, sources may be misread, and a confident-looking
classification can still be wrong. Double-check every criterion and
its underlying evidence before relying on any call.
Gene diagram
· NM_006231.4 · variants mapped to exon structure
POLENM_006231.4
Fetching transcript structure from UCSC…
Exons
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Transcript span
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Strand
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Variants mapped
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Source
UCSC ncbiRefSeqCurated
All variants in POLE—click a row to locate it on the plot · use the link column to open its page
Protein
Location
Classification
Link
Applied criteria · 2 applied · 18 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 2
Strength Supporting Moderate Strong Very strong
✓
PM2supportingPathogenic
Met (supporting): absent from gnomAD v2.1, v4.1, and gnomAD-Canada, satisfying the 'absent in controls' population criterion.
Met (supporting): synonymous p.Ser988= with SpliceAI max delta 0.01, far below the 0.2 impact threshold, predicting no splice effect.
spliceai: SpliceAI max delta score 0.01 (DS_AG 0.01, DS_AL 0.0, DS_DG 0.0, DS_DL 0.0) for NM_006231.4:c.2964G>T (SpliceAI Lookup, Broad Institute, distance=500, basic mode); below the 0.2 high-impact delta threshold (Jaganathan et al. 2019, PMID 30661751), predicting no splice impact and no new splice-site creation.pvs1_variant_assessment: consequence_class='synonymous', protein NP_006222.2:p.(Ser988=), canonical_splice_consensus=false.generic_acmg_combination_rules: BP7 criterion from Richards et al. 2015 (PMID 25741868) - synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site.
Assessed · not applied
· 8 not met · 10 not assessed
Pathogenic
PS2Not assessed: no de novo occurrence with confirmed parental testing is documented in ClinVar or the literature.
PS3Not assessed: no functional assay of this variant exists; the only related data is an in silico SpliceAI prediction (max delta 0.01), not a functional study.
PS4Not met: the gene-specific rule applies only to recurrent missense variants (none at residue 988), and no case-control study exists for this variant.
PM3Not assessed: no proband genotype or phase data exist to evaluate a trans configuration with a pathogenic variant.
PM6Not assessed: no de novo occurrence, with or without parentage confirmation, is documented for this variant.
PP1Not assessed: no segregation study or family testing data exists — zero informative meioses are documented.
PP3Not met: SpliceAI predicts no splice impact (max delta 0.01), the only predictor available, so no computational evidence supports a deleterious effect.
PP4Not assessed: no proband phenotype or family-history data for a carrier of this variant is available.
PP5Not met: no ClinVar expert-panel (3-star) pathogenic classification exists; the only submission is a 1-star laboratory 'Likely benign'.
Benign
BA1Not met: the variant is absent (frequency 0) from gnomAD v2.1, v4.1, and gnomAD-Canada, so no population threshold is exceeded.
BS1Not met: observed frequency is 0 in all three population databases, the opposite of a frequency greater than expected.
BS2Not met: no healthy adult carriers or homozygotes are observed; the variant is absent from all three population databases.
BS3Not assessed: no functional studies of this variant exist; in silico and population data cannot substitute for them.
BS4Not assessed: no affected family member has been tested and reported as not carrying the variant.
BP2Not assessed: no genotype data exists to establish a trans or cis configuration with a pathogenic variant.
BP4Not met: the only 'no impact' prediction (SpliceAI max delta 0.01) is already counted under BP7; no independent benign computational line exists.
BP5Not assessed: no reported carrier with an alternate molecular basis exists, so an alternate diagnosis can be neither established nor excluded.
BP6Not met: the 'Likely benign' label is a 1-star laboratory submission, not an expert-panel classification, so BP6 does not apply.
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why.
Rule & framework references · cited for criterion definitions, not variant evidence
25394175 ↗A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment.